This directory contains genotypes for the Vindija, Altai and Denisova genomes
generated using snpAD, an ancient DNA damage-aware genotyper developed in
Leipzig for the analysis of the Vindija genome. The genotyper uses an empircal
error profile that captures the position-dependent probabilities of base
exchanges due to error and deamination to estimate the proportion of all
possible genotypes by maximum likelihood. Using these estimate as priors the
posterior genotype probability is calculated and the genotype with the the
highest likelihood is reported at each position. Estimates were restricted to
mappable regions (Heng Li's 35mer filter: a position is mappable if none of the
overlapping 35mers align to any other position in the genome allowing for up to
one mismatch) and required a MQ>=25 on sequences.

The human genome hg19/GRCh37 was used as reference in all VCFs. See
../bam/README for further details on alignments and reference genome.

Contact: <Kay Pruefer> pruefer@eva.mpg.de